metawatt / Discussion / General Discussion: Create all genomes taxonomy DB

Lizbeth Sayavedra - 2012-11-27

Hi Marc,
I don't know if this is a problem related to Mac, but when I use the function "create all genomes taxonomy DB" the program stops in the genome 52 from the all.gbk folder (downloaded from NCBI), and it has a legend with "done" although 0% is completed. Is this normal?
Best,
Lizbeth

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- Christopher Carr - 2013-01-24
  
  I have the same problem... stops on genome 53. Button changes from "Cancel" to "Close" and label above progress bar changes to "done".... then nothing happens.
  
  Also, for the author... the dialog with title "Select taxonomy db file" is very counterintuitive. It should just present a "Save As" dialog box. I finally made a text file called "taxonomy.txt" and selected it but it was not at all clear what the user should do.
  
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  - Marc Strous - 2013-01-25
    
    Dear Christopher,
    
    I have the same problem... stops on genome 53. Button changes from
    "Cancel"
    to "Close" and label above progress bar changes to "done".... then
    nothing
    happens.
    I have tried to debug this one before, but no luck yet. What system are you
    using and what language/locale?
    
    In the next version I will use a different parser for this task. For now,
    maybe you can try if you can use the attached taxonomy file. It was created
    this week with the latest all.tar.gz file downloaded from genbank and also
    includes draft genomes. With this file you should be able to create your
    blastdb, even if you do not have the draft genomes present. Let me know if
    it works.
    
    Also, for the author... the dialog with title "Select taxonomy db file"
    is
    very counterintuitive. It should just present a "Save As" dialog box. I
    finally made a text file called "taxonomy.txt" and selected it but it was
    not at all clear what the user should do.
    Good point. Will be changed in next version. You do not need to create the
    file, it should really be "save as" as you suggested
    
    Best wishes,
    Marc
    
    [Create all genomes taxonomy
    
    DB](https://sourceforge.net/p/metawatt/discussion/general/thread/aed4ea2d/?limit=25#a709/c0b7)
    
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  - Marc Strous - 2013-01-25
    
    Ok, I think the forum does not accept attachments. So I added the taxonomy
    file as a separate file in the files area.
    By the way: Lizbeth avoided the problem by simply removing the genomes that
    caused the problem.
    Marc
    
    On Thu, 24 Jan 2013 23:59:43 +0000, "Christopher Carr"
    carrce@users.sf.net
    wrote:
    
    I have the same problem... stops on genome 53. Button changes from
    "Cancel"
    to "Close" and label above progress bar changes to "done".... then
    nothing
    happens.
    
    Also, for the author... the dialog with title "Select taxonomy db file"
    is
    very counterintuitive. It should just present a "Save As" dialog box. I
    finally made a text file called "taxonomy.txt" and selected it but it was
    not at all clear what the user should do.
    
    [Create all genomes taxonomy
    
    DB](https://sourceforge.net/p/metawatt/discussion/general/thread/aed4ea2d/?limit=25#a709/c0b7)
    
    Sent from sourceforge.net because you indicated interest in
    https://sourceforge.net/p/metawatt/discussion/general/
    
    To unsubscribe from further messages, please visit
    https://sourceforge.net/auth/prefs/
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Create all genomes taxonomy DB

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Create all genomes taxonomy DB

Create all genomes taxonomy DB

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Create all genomes taxonomy DB